Buggy code:
public class LabelAdder { private static final String QUERY_NAME = "PREFIX<seq2seq4repair_space>gn:<seq2seq4repair_space><http:////www.geonames.org//ontology#>\n" + ( ( ( "SELECT<seq2seq4repair_space>?name<seq2seq4repair_space>?parent<seq2seq4repair_space>WHERE<seq2seq4repair_space>{\n" + "<seq2seq4repair_space>?place<seq2seq4repair_space>gn:name<seq2seq4repair_space>?name.\n" ) + "<seq2seq4repair_space>?place<seq2seq4repair_space>gn:parentFeature<seq2seq4repair_space>?parent.\n" ) + "}" ) ; public static void main ( String [ ] args ) { if ( ( args . length ) != 3 ) { System . out . println ( ( ( "USAGE:<seq2seq4repair_space>java<seq2seq4repair_space>" + ( LabelAdder . class . getName ( ) ) ) + "<seq2seq4repair_space><repo<seq2seq4repair_space>dir><seq2seq4repair_space><input<seq2seq4repair_space>file><seq2seq4repair_space><output<seq2seq4repair_space>file>" ) ) ; System . exit ( 0 ) ; } File repoDir = new File ( args [ 0 ] ) ; File inputFile = new File ( args [ 1 ] ) ; File outputFile = new File ( args [ 2 ] ) ; try { NativeStore store = new NativeStore ( repoDir ) ; Repository repository = new org . openrdf . repository . sail . SailRepository ( store ) ; repository . initialize ( ) ; RepositoryConnection connection = repository . getConnection ( ) ; FileReader fileReader = new FileReader ( inputFile ) ; BufferedReader bufferedReader = new BufferedReader ( fileReader ) ; FileWriter fileWriter = new FileWriter ( outputFile ) ; BufferedWriter bufferedWriter = new BufferedWriter ( fileWriter ) ; try { String line = bufferedReader . readLine ( ) ; if ( line == null ) { System . err . println ( ( "input<seq2seq4repair_space>file<seq2seq4repair_space>is<seq2seq4repair_space>empty:<seq2seq4repair_space>" + ( inputFile . getAbsolutePath ( ) ) ) ) ; System . exit ( 1 ) ; } bufferedWriter . write ( ( ( ( "lineage" + ( Reconciler . COLUMN_SEPARATOR ) ) + line ) + "\n" ) ) ; while ( ( line = bufferedReader . readLine ( ) ) != null ) { String [ ] fields = COLUMN_SPLITTER . split ( line ) ; if ( ( fields [ 0 ] . length ( ) ) == 0 ) <START_BUG> continue ; <END_BUG> String [ ] places = LIST_SPLITTER . split ( fields [ 0 ] ) ; StringBuilder lineages = new StringBuilder ( ) ; for ( String place : places ) { URL placeURL = new URL ( place ) ; lineages . append ( LIST_SEPARATOR ) ; lineages . append ( LabelAdder . lineage ( connection , placeURL ) ) ; } bufferedWriter . write ( ( ( ( ( lineages . substring ( LIST_SEPARATOR . length ( ) ) ) + ( Reconciler . COLUMN_SEPARATOR ) ) + line ) + "\n" ) ) ; } } catch ( IOException e ) { e . printStackTrace ( ) ; } catch ( QueryEvaluationException e ) { e . printStackTrace ( ) ; } catch ( MalformedQueryException e ) { e . printStackTrace ( ) ; } finally { bufferedWriter . close ( ) ; fileWriter . close ( ) ; bufferedReader . close ( ) ; fileReader . close ( ) ; connection . close ( ) ; repository . shutDown ( ) ; store . shutDown ( ) ; } } catch ( RepositoryException e ) { e . printStackTrace ( ) ; } catch ( SailException e ) { e . printStackTrace ( ) ; } catch ( FileNotFoundException e ) { e . printStackTrace ( ) ; } catch ( IOException e ) { e . printStackTrace ( ) ; } } private static String lineage ( RepositoryConnection connection , URL placeURL ) throws MalformedQueryException , QueryEvaluationException , MalformedURLException , RepositoryException { } }

Fix:
bufferedWriter . write ( ( ( ( Reconciler . COLUMN_SEPARATOR ) + line ) + "\n" ) ) ;